Pufferfish: Sushi or Science?

Kristen Philipkoski
06.12.00

A researcher in Berkeley, California is mapping the genome of the pufferfish, despite having practically no funds to finish the project.

Sydney Brenner of the Molecular Science Institute believes that deciphering the genes of the Japanese delicacy is the fastest way to help researchers locate human genes, because its genome has no superfluous material.

In humans, the part of the genome that makes up active genes is only about 3 percent. The rest is called "junk DNA," although scientists argue about whether junk DNA has any function. The pufferfish, however, has practically no junk DNA. The pufferfish, also known as Fugu, and the human genome both have about the same number of genes -- about 50,000 by Brenner's estimation (there is much debate over how many genes there actually are). All of the Fugu DNA is compressed into only about 375 million chemical letters, while humans have more than 3 billion.

Brenner believes this is key to the pufferfish's importance. It will be more expensive and take longer using the mouse or zebrafish models - currently being mapped in government-funded labs -- because researchers first have to sift through the junk, according to Brenner.

When researchers discover genes in the pufferfish, they can compare it to a human and find the same gene to determine its function.

Human genome researchers say that the pufferfish certainly has potential as a model for genes, but since organisms like the mouse and the zebrafish have been studied so much in the past, they are more likely candidates for government funds.

"(The pufferfish) is certainly devoid of repeats and that makes it a less costly thing to approach, but that's not necessarily on its own compelling," said Richard Gibbs, director of the gene sequencing lab at the Baylor College of Medicine in Houston.

Supply of the pufferfish is not a problem. They are raised in bulk on fish farms in Japan. The delicacy is extraordinarily popular at posh restaurants even though, if prepared improperly, eating the fish can be lethal.

Money to fund the research, on the other hand, is not forthcoming.

Brenner refers to his molecular science lab is the only privately owned genome project in the world, since he gets no funding.

Less than 1 percent of the pufferfish sequence has so far been completed, but any of the large sequencing centers could probably complete the entire project in a matter of months.

Most of the funds for this type of research are going toward projects to map the mouse and zebrafish genomes. Researchers can use these model organisms to discover the function of genes, and match them to human genes.

But Brenner believes the pufferfish will make a better model.

Other organisms used as models, such as yeast, the fruit fly and the nemotode worm, will be even more difficult to compare to humans than vertebrates because evolution has preserved fewer genes between humans and these species.

"It depends on what you want to get form the research. The attraction of the mouse and the fruit fly is they are very well established and powerful experimental systems in their own right," Gibbs said.

Another plus to studying the pufferfish, according to Brenner, is that genes are physically close together in the Fugu genome, are often also in close proximity in the human genome. Brenner estimates that up to ten genes at a time might be conserved between the two species.

Gibbs said there's room for a genome map of all important creatures. With high-speed genome sequencers now available, it's no longer the huge undertaking it once was to map an organism's genome.

"Now we're starting to say we better get these genomes in the queue," he said. "So maybe we shouldn't belabor the debate over whether the pufferfish versus the mouse should come first so mush as let's get on with all of it."